New sequence types and multidrug resistance among pathogenic Escherichia coli isolates from coastal marine sediments

Abstract

The spread of antibiotic-resistant microorganisms is widely recognized, but data about their sources, presence, and significance in marine environments are still limited. We examined 109 Escherichia coli strains from coastal marine sediments carrying virulence genes for antibiotic susceptibility, specific resistance genes, prevalence of class 1 and 2 integrons, and sequence type. Antibiotic resistance was found in 35% of strains, and multiple resistances were found in 14%; the resistances detected most frequently were against tetracycline (28%), ampicillin (16.5%), trimethoprim-sulfamethoxazole (13%), and streptomycin (7%). The highest prevalence of resistant strains was in phylogenetic group A, whereas phylogroup B2 exhibited a significantly lower frequency than all the other groups. Sixty percent of multiresistant strains harbored class 1 or 2 integrase genes, and about 50% carried resistance genes (particularly dfrA and aadA) linked to a class 1 integron. Multilocus sequence typing of 14 selected strains identified eight different types characteristic of extraintestinal pathogens and three new allelic combinations. Our data suggest that coastal marine sediment may be a suitable environment for the survival of pathogenic and antimicrobial-resistant E. coli strains capable of contributing to resistance spread via integrons among benthic bacteria, and they highlight a role for these strains in the emergence of new virulent genotypes.

Fig 1

Antimicrobial resistances detected in 109 E. coli strains from four phylogenetic groups (A, B1, B2, and D). Group A, 38 strains; group B1, 27 strains; group B2, 21 strains; group D, 23 strains.

Fig 2

Prevalence of MDR strains among the 109 E. coli isolates analyzed in this study.

Fig 3

Population snapshot showing the clusters of related ST and the individual unrelated ST within the MLST E. coli database (3,725 isolates). The ST indicated are those found in this study. The three new ST are boxed.